Multiple sequence alignment - TraesCS3D01G166800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3D01G166800 chr3D 100.000 4570 0 0 1 4570 141177980 141182549 0.000000e+00 8440.0
1 TraesCS3D01G166800 chr3D 75.000 212 31 17 4376 4570 496045450 496045244 1.360000e-10 78.7
2 TraesCS3D01G166800 chr3D 75.862 174 26 10 4377 4536 384730625 384730454 1.760000e-09 75.0
3 TraesCS3D01G166800 chr3A 94.089 3434 151 29 603 4016 159346938 159350339 0.000000e+00 5169.0
4 TraesCS3D01G166800 chr3A 93.111 479 20 4 1 477 159343336 159343803 0.000000e+00 689.0
5 TraesCS3D01G166800 chr3A 87.805 246 19 5 4041 4282 159350617 159350855 1.250000e-70 278.0
6 TraesCS3D01G166800 chr3A 83.333 282 28 14 4293 4560 159351143 159351419 4.570000e-60 243.0
7 TraesCS3D01G166800 chr3A 95.205 146 6 1 474 619 159344067 159344211 3.560000e-56 230.0
8 TraesCS3D01G166800 chr3B 94.858 2003 77 19 494 2484 202898924 202900912 0.000000e+00 3105.0
9 TraesCS3D01G166800 chr3B 89.439 1979 147 32 2465 4429 202900924 202902854 0.000000e+00 2440.0
10 TraesCS3D01G166800 chr3B 88.636 132 8 5 4441 4568 202902904 202903032 2.200000e-33 154.0
11 TraesCS3D01G166800 chr6A 77.059 170 24 10 4381 4536 350839382 350839550 2.930000e-12 84.2
12 TraesCS3D01G166800 chr1D 91.667 48 4 0 4376 4423 450056170 450056217 2.950000e-07 67.6
13 TraesCS3D01G166800 chr1D 100.000 29 0 0 4542 4570 296075114 296075086 2.000000e-03 54.7
14 TraesCS3D01G166800 chr5D 96.970 33 1 0 4538 4570 276472247 276472215 6.390000e-04 56.5
15 TraesCS3D01G166800 chr5A 100.000 29 0 0 4542 4570 167119218 167119246 2.000000e-03 54.7
16 TraesCS3D01G166800 chr2D 96.970 33 0 1 4538 4570 488236106 488236075 2.000000e-03 54.7
17 TraesCS3D01G166800 chr2B 96.970 33 0 1 4538 4570 572592706 572592675 2.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G166800 chr3D 141177980 141182549 4569 False 8440.000000 8440 100.000000 1 4570 1 chr3D.!!$F1 4569
1 TraesCS3D01G166800 chr3A 159343336 159351419 8083 False 1321.800000 5169 90.708600 1 4560 5 chr3A.!!$F1 4559
2 TraesCS3D01G166800 chr3B 202898924 202903032 4108 False 1899.666667 3105 90.977667 494 4568 3 chr3B.!!$F1 4074

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
65 66 0.179032 TGCCTCTTGCTCCGAACAAA 60.179 50.0 0.00 0.0 42.00 2.83 F
103 104 0.243636 CCTGCGTTGGGGAACAATTC 59.756 55.0 0.00 0.0 41.95 2.17 F
847 3862 0.523519 GGCGCCTCTTCTTCAAAAGG 59.476 55.0 22.15 0.0 0.00 3.11 F
1675 4699 0.820891 GTAGGGCCTCACGTATCCGA 60.821 60.0 10.74 0.0 37.88 4.55 F
2584 5643 0.981183 TACCAGGCAAATCCACGACT 59.019 50.0 0.00 0.0 37.29 4.18 F
3010 6072 0.531974 GCAGGAGTGTCCGTTCACAA 60.532 55.0 9.28 0.0 42.75 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1722 4746 0.036164 ACAGACCAATAAGCGTGCCA 59.964 50.0 0.00 0.0 0.00 4.92 R
2097 5125 2.368875 CCACCCTACAGAAGACAAGTGT 59.631 50.0 0.00 0.0 0.00 3.55 R
2674 5733 2.103094 CTCTGAAACCGGATGGATAGCA 59.897 50.0 9.46 0.0 39.21 3.49 R
2986 6048 0.108585 AACGGACACTCCTGCAACAT 59.891 50.0 0.00 0.0 33.30 2.71 R
3407 6473 0.111253 AGGTTTGTCTCTGCAAGGGG 59.889 55.0 0.00 0.0 32.73 4.79 R
4315 7918 0.253327 ATGCCCTCGAAAGGAGAACC 59.747 55.0 5.34 0.0 46.67 3.62 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 2.902486 AGCATGAGTGAGAGAAGGTTCA 59.098 45.455 0.00 0.00 0.00 3.18
53 54 1.075601 TTCAGGTTGGGATGCCTCTT 58.924 50.000 4.35 0.00 31.73 2.85
65 66 0.179032 TGCCTCTTGCTCCGAACAAA 60.179 50.000 0.00 0.00 42.00 2.83
66 67 0.951558 GCCTCTTGCTCCGAACAAAA 59.048 50.000 0.00 0.00 36.87 2.44
67 68 1.541588 GCCTCTTGCTCCGAACAAAAT 59.458 47.619 0.00 0.00 36.87 1.82
68 69 2.029918 GCCTCTTGCTCCGAACAAAATT 60.030 45.455 0.00 0.00 36.87 1.82
69 70 3.568538 CCTCTTGCTCCGAACAAAATTG 58.431 45.455 0.00 0.00 0.00 2.32
70 71 3.004734 CCTCTTGCTCCGAACAAAATTGT 59.995 43.478 0.00 0.00 44.72 2.71
71 72 7.956127 GCCTCTTGCTCCGAACAAAATTGTT 62.956 44.000 11.09 11.09 44.85 2.83
85 86 4.736126 AAATTGTTCGATCAATTCCCCC 57.264 40.909 26.51 0.00 44.10 5.40
101 102 1.606313 CCCTGCGTTGGGGAACAAT 60.606 57.895 6.93 0.00 46.50 2.71
103 104 0.243636 CCTGCGTTGGGGAACAATTC 59.756 55.000 0.00 0.00 41.95 2.17
104 105 0.958091 CTGCGTTGGGGAACAATTCA 59.042 50.000 0.00 0.00 41.95 2.57
153 155 3.199677 CGTTCGGGCCTTAACATCAATA 58.800 45.455 17.26 0.00 0.00 1.90
162 164 5.754890 GGCCTTAACATCAATAAGCCAAATG 59.245 40.000 0.00 0.00 32.02 2.32
225 227 4.748102 ACGTTCACACATCTCGTAAATTGT 59.252 37.500 0.00 0.00 33.04 2.71
326 328 6.648725 TGCACAAAAATTAGCCCAAATTAGAC 59.351 34.615 0.00 0.00 0.00 2.59
342 344 4.462508 TTAGACAGATGCTTGAGAGGTG 57.537 45.455 0.00 0.00 0.00 4.00
377 379 1.831580 CAAGGCTCCTTGCTTAGCTT 58.168 50.000 14.94 0.00 45.38 3.74
382 384 3.200825 AGGCTCCTTGCTTAGCTTAATCA 59.799 43.478 5.60 0.00 42.39 2.57
383 385 4.140536 GGCTCCTTGCTTAGCTTAATCAT 58.859 43.478 5.60 0.00 42.39 2.45
414 416 7.173218 CACTTTAAGTGTCACATGAACCAGTAT 59.827 37.037 16.22 0.00 41.19 2.12
421 423 5.943416 TGTCACATGAACCAGTATTTTAGGG 59.057 40.000 0.00 0.00 0.00 3.53
423 425 6.657541 GTCACATGAACCAGTATTTTAGGGAA 59.342 38.462 0.00 0.00 0.00 3.97
425 427 7.175990 TCACATGAACCAGTATTTTAGGGAAAC 59.824 37.037 0.00 0.00 0.00 2.78
455 458 7.494625 ACTTGATTTGACAGTTTTTAGAGACGA 59.505 33.333 0.00 0.00 0.00 4.20
457 460 7.851508 TGATTTGACAGTTTTTAGAGACGAAG 58.148 34.615 0.00 0.00 0.00 3.79
477 480 5.115773 CGAAGAACGAGTAGTTGAAGAACAG 59.884 44.000 0.00 0.00 44.35 3.16
480 483 5.978322 AGAACGAGTAGTTGAAGAACAGAAC 59.022 40.000 0.00 0.00 44.35 3.01
483 486 6.670233 ACGAGTAGTTGAAGAACAGAACTAG 58.330 40.000 0.00 0.00 34.17 2.57
485 488 7.443575 ACGAGTAGTTGAAGAACAGAACTAGTA 59.556 37.037 0.00 0.00 31.72 1.82
487 490 9.562583 GAGTAGTTGAAGAACAGAACTAGTATG 57.437 37.037 0.00 0.67 34.17 2.39
632 3643 3.061848 TTAGCAGCCAAAGCGCCC 61.062 61.111 2.29 0.00 46.67 6.13
823 3838 3.011517 CCCCCACCACCAGAGAGG 61.012 72.222 0.00 0.00 45.67 3.69
847 3862 0.523519 GGCGCCTCTTCTTCAAAAGG 59.476 55.000 22.15 0.00 0.00 3.11
870 3886 1.202722 TCCCTTTTCTTTTCTCGGCGT 60.203 47.619 6.85 0.00 0.00 5.68
969 3986 2.677228 CTAGGCTGGTTGGTGGGG 59.323 66.667 0.00 0.00 0.00 4.96
1297 4315 3.814268 CGCTTGATTGTGGCCCCG 61.814 66.667 0.00 0.00 0.00 5.73
1305 4323 1.635817 ATTGTGGCCCCGCTATGTCT 61.636 55.000 0.00 0.00 0.00 3.41
1315 4333 2.101415 CCCGCTATGTCTCTGTCAATCA 59.899 50.000 0.00 0.00 0.00 2.57
1330 4348 6.547141 TCTGTCAATCACAAGATTTTGTTCCT 59.453 34.615 0.00 0.00 45.01 3.36
1408 4426 6.992063 ACTTAGTGTGCTCATAATTTCTGG 57.008 37.500 0.00 0.00 0.00 3.86
1415 4433 6.018669 GTGTGCTCATAATTTCTGGTAGTAGC 60.019 42.308 0.00 0.00 0.00 3.58
1451 4474 1.400494 CCTTTTGCCGTACCATGTAGC 59.600 52.381 0.00 0.00 0.00 3.58
1475 4498 8.428063 AGCTGTATGTCTAATCTTCTATTGCTT 58.572 33.333 0.00 0.00 0.00 3.91
1476 4499 8.494347 GCTGTATGTCTAATCTTCTATTGCTTG 58.506 37.037 0.00 0.00 0.00 4.01
1549 4572 1.906966 CAATTGAGCAAAAGCGCTACG 59.093 47.619 12.05 2.78 44.01 3.51
1672 4696 2.579873 TGTAGTAGGGCCTCACGTATC 58.420 52.381 10.74 0.00 0.00 2.24
1675 4699 0.820891 GTAGGGCCTCACGTATCCGA 60.821 60.000 10.74 0.00 37.88 4.55
1722 4746 3.340814 ACTGTAGCTTAGTTGCATGCT 57.659 42.857 20.33 0.40 39.30 3.79
1758 4782 4.992951 GGTCTGTTTATGTCAACCGTTAGT 59.007 41.667 0.00 0.00 0.00 2.24
1762 4786 5.358090 TGTTTATGTCAACCGTTAGTGTGA 58.642 37.500 0.00 0.00 0.00 3.58
2052 5080 7.662604 TTAATTCTTCGGTCTCTTGTTTACC 57.337 36.000 0.00 0.00 0.00 2.85
2097 5125 7.757173 GCTATCTCGTATCTTGCATCTCATTTA 59.243 37.037 0.00 0.00 0.00 1.40
2268 5296 2.358939 ATCGTCGGTTGAACAGGTAC 57.641 50.000 0.00 0.00 0.00 3.34
2270 5298 1.682854 TCGTCGGTTGAACAGGTACTT 59.317 47.619 0.00 0.00 34.60 2.24
2294 5322 7.664552 TTAATTGAATGCTGAATGAAGGGAT 57.335 32.000 0.00 0.00 0.00 3.85
2295 5323 6.555463 AATTGAATGCTGAATGAAGGGATT 57.445 33.333 0.00 0.00 0.00 3.01
2296 5324 6.555463 ATTGAATGCTGAATGAAGGGATTT 57.445 33.333 0.00 0.00 0.00 2.17
2297 5325 6.363167 TTGAATGCTGAATGAAGGGATTTT 57.637 33.333 0.00 0.00 0.00 1.82
2299 5327 6.167685 TGAATGCTGAATGAAGGGATTTTTG 58.832 36.000 0.00 0.00 0.00 2.44
2300 5328 5.750352 ATGCTGAATGAAGGGATTTTTGT 57.250 34.783 0.00 0.00 0.00 2.83
2301 5329 5.549742 TGCTGAATGAAGGGATTTTTGTT 57.450 34.783 0.00 0.00 0.00 2.83
2302 5330 5.927819 TGCTGAATGAAGGGATTTTTGTTT 58.072 33.333 0.00 0.00 0.00 2.83
2303 5331 6.355747 TGCTGAATGAAGGGATTTTTGTTTT 58.644 32.000 0.00 0.00 0.00 2.43
2304 5332 6.260493 TGCTGAATGAAGGGATTTTTGTTTTG 59.740 34.615 0.00 0.00 0.00 2.44
2577 5636 5.449304 GCGTTACATATTACCAGGCAAATC 58.551 41.667 0.00 0.00 0.00 2.17
2584 5643 0.981183 TACCAGGCAAATCCACGACT 59.019 50.000 0.00 0.00 37.29 4.18
2674 5733 3.169099 AGGCGCAGATATAGTGGAATCT 58.831 45.455 10.83 0.00 32.63 2.40
2794 5853 4.764823 AGTTCTGAGTTCTCGAGAGATTGT 59.235 41.667 15.94 0.00 40.84 2.71
2876 5937 2.101582 GACAACGATGAGGTAGGCAGAT 59.898 50.000 0.00 0.00 0.00 2.90
2906 5968 2.479656 GGACCGTGTTTGCGTGTTATTA 59.520 45.455 0.00 0.00 0.00 0.98
2929 5991 9.685276 ATTATGGATCAAAGTGTTCATAAGACA 57.315 29.630 0.00 0.00 0.00 3.41
2932 5994 5.123979 GGATCAAAGTGTTCATAAGACACCC 59.876 44.000 3.96 0.00 35.17 4.61
2934 5996 5.690865 TCAAAGTGTTCATAAGACACCCTT 58.309 37.500 3.96 0.00 38.87 3.95
2939 6001 6.306987 AGTGTTCATAAGACACCCTTTTGAT 58.693 36.000 3.96 0.00 40.70 2.57
2949 6011 4.441792 ACACCCTTTTGATTGTTCTTTGC 58.558 39.130 0.00 0.00 0.00 3.68
2963 6025 8.986477 ATTGTTCTTTGCCAAAATAGACATAC 57.014 30.769 0.00 0.00 0.00 2.39
2966 6028 9.461312 TGTTCTTTGCCAAAATAGACATACTAT 57.539 29.630 0.00 0.00 42.86 2.12
3010 6072 0.531974 GCAGGAGTGTCCGTTCACAA 60.532 55.000 9.28 0.00 42.75 3.33
3016 6078 1.971357 AGTGTCCGTTCACAATCTCCT 59.029 47.619 9.28 0.00 40.37 3.69
3017 6079 3.162666 AGTGTCCGTTCACAATCTCCTA 58.837 45.455 9.28 0.00 40.37 2.94
3121 6183 6.488683 TCGTGAACTTGAATCCAAAAGGTATT 59.511 34.615 0.00 0.00 0.00 1.89
3150 6212 8.883731 AGTAATTCTGATCTTACATTTGAACGG 58.116 33.333 11.10 0.00 31.64 4.44
3151 6213 7.687941 AATTCTGATCTTACATTTGAACGGT 57.312 32.000 0.00 0.00 0.00 4.83
3156 6218 4.742438 TCTTACATTTGAACGGTCAAGC 57.258 40.909 16.64 0.00 44.49 4.01
3174 6236 1.610522 AGCGCTGCTTTCTTTGAATGT 59.389 42.857 10.39 0.00 33.89 2.71
3198 6262 4.378253 GCAGCTTGCTGAAGAGAACTTAAG 60.378 45.833 24.67 0.00 40.96 1.85
3244 6308 0.808755 CAGGTTCGCCAATACCAACC 59.191 55.000 0.00 0.00 40.60 3.77
3245 6309 0.675522 AGGTTCGCCAATACCAACCG 60.676 55.000 0.00 0.00 42.77 4.44
3364 6428 8.837059 GCGTTATTTCTGTTTAACAGTGTATTG 58.163 33.333 22.36 10.85 46.03 1.90
3536 6602 2.311688 GACGCCGGTGGAGGAATGAT 62.312 60.000 21.14 0.00 0.00 2.45
3606 6674 3.117701 TGGATCTTGTTCCTTGTTGACCA 60.118 43.478 0.00 0.00 36.68 4.02
3625 6693 4.181578 ACCAAATCTCGTTCCTTCATACG 58.818 43.478 0.00 0.00 39.03 3.06
3626 6694 4.081862 ACCAAATCTCGTTCCTTCATACGA 60.082 41.667 0.00 0.00 43.73 3.43
3660 6728 3.699779 TCGAGATCTCAGACCAAATCG 57.300 47.619 22.31 5.51 0.00 3.34
3693 6761 8.593492 TCATACATATAGCTTGTGTGTCATTC 57.407 34.615 11.93 0.00 37.44 2.67
3710 6778 7.282901 TGTGTCATTCCCATGTGTTTATAGATG 59.717 37.037 0.00 0.00 0.00 2.90
3774 6842 1.538075 CAAGCACATGACACATGAGCA 59.462 47.619 25.96 0.00 37.94 4.26
3786 6854 5.125100 ACACATGAGCAAACCAAATACAG 57.875 39.130 0.00 0.00 0.00 2.74
3811 6879 4.814147 CTCAGATGAGCAACTTCAGTACA 58.186 43.478 0.00 0.00 35.13 2.90
3843 6911 4.881850 ACATACATCCATTTCCCGTTTCTC 59.118 41.667 0.00 0.00 0.00 2.87
3857 6925 3.637229 CCGTTTCTCTGGCCTAGATCTTA 59.363 47.826 3.32 0.00 34.21 2.10
3882 6950 3.968265 CCAAATACATGGTGGTCCTTCT 58.032 45.455 0.00 0.00 35.65 2.85
3883 6951 3.696051 CCAAATACATGGTGGTCCTTCTG 59.304 47.826 0.00 0.00 35.65 3.02
3904 6972 4.277476 TGGTGTCATTTTCCTCTGTTTGT 58.723 39.130 0.00 0.00 0.00 2.83
3955 7023 1.228737 GGGCTGGTTTTGTGGCCTA 60.229 57.895 3.32 0.00 43.62 3.93
4025 7260 6.224584 GTCCCTAAACTAATAGATCCACTGC 58.775 44.000 0.00 0.00 0.00 4.40
4081 7404 8.325787 AGTTGTATCCATACAGTAATCCAACAA 58.674 33.333 0.00 1.60 43.44 2.83
4103 7426 0.969894 ACACTTGCTAGGTCGCTCTT 59.030 50.000 0.00 0.00 0.00 2.85
4104 7427 1.067495 ACACTTGCTAGGTCGCTCTTC 60.067 52.381 0.00 0.00 0.00 2.87
4105 7428 0.533032 ACTTGCTAGGTCGCTCTTCC 59.467 55.000 0.00 0.00 0.00 3.46
4106 7429 0.820871 CTTGCTAGGTCGCTCTTCCT 59.179 55.000 0.00 0.00 37.80 3.36
4107 7430 0.818296 TTGCTAGGTCGCTCTTCCTC 59.182 55.000 0.00 0.00 35.51 3.71
4108 7431 0.033991 TGCTAGGTCGCTCTTCCTCT 60.034 55.000 0.00 0.00 35.51 3.69
4170 7495 0.895530 CACTTCTCCGAGCCCACTAA 59.104 55.000 0.00 0.00 0.00 2.24
4171 7496 1.134965 CACTTCTCCGAGCCCACTAAG 60.135 57.143 0.00 0.00 0.00 2.18
4175 7500 4.176752 CCGAGCCCACTAAGCCCC 62.177 72.222 0.00 0.00 0.00 5.80
4177 7502 2.670148 CGAGCCCACTAAGCCCCTT 61.670 63.158 0.00 0.00 0.00 3.95
4178 7504 1.224870 GAGCCCACTAAGCCCCTTC 59.775 63.158 0.00 0.00 0.00 3.46
4182 7508 1.550179 GCCCACTAAGCCCCTTCTTTT 60.550 52.381 0.00 0.00 0.00 2.27
4203 7529 2.559698 TCTTCATTTCCTTCCGTGCA 57.440 45.000 0.00 0.00 0.00 4.57
4209 7535 3.129113 TCATTTCCTTCCGTGCAATCATG 59.871 43.478 0.00 0.00 0.00 3.07
4218 7544 2.287188 CCGTGCAATCATGTCATTAGGC 60.287 50.000 0.00 0.00 0.00 3.93
4221 7547 3.881688 GTGCAATCATGTCATTAGGCTCT 59.118 43.478 0.00 0.00 0.00 4.09
4229 7555 5.768164 TCATGTCATTAGGCTCTACACGATA 59.232 40.000 0.00 0.00 0.00 2.92
4230 7556 6.434340 TCATGTCATTAGGCTCTACACGATAT 59.566 38.462 0.00 0.00 0.00 1.63
4288 7614 4.155826 TGTCAGCCAACTTTCCATTAATCG 59.844 41.667 0.00 0.00 0.00 3.34
4307 7910 0.249447 GTGTTCAGCCAACCTTTGCC 60.249 55.000 0.00 0.00 33.51 4.52
4315 7918 0.035176 CCAACCTTTGCCCATTGTGG 59.965 55.000 0.00 0.00 37.25 4.17
4379 7982 5.441718 TCCATTTTCATCTTGAGTAGGCT 57.558 39.130 0.00 0.00 0.00 4.58
4407 8010 4.797471 TGATTTGCAGGATTCTCAAAACG 58.203 39.130 3.65 0.00 34.00 3.60
4408 8011 3.641437 TTTGCAGGATTCTCAAAACGG 57.359 42.857 0.00 0.00 0.00 4.44
4437 8053 2.008242 AAAAATACAGGCTGCCCACA 57.992 45.000 16.57 0.00 0.00 4.17
4438 8054 1.256812 AAAATACAGGCTGCCCACAC 58.743 50.000 16.57 0.00 0.00 3.82
4451 8067 1.002087 GCCCACACGAATCCTATAGGG 59.998 57.143 18.97 5.11 38.10 3.53
4455 8071 4.384868 CCCACACGAATCCTATAGGGTTTT 60.385 45.833 18.54 10.00 38.97 2.43
4456 8072 5.163280 CCCACACGAATCCTATAGGGTTTTA 60.163 44.000 18.54 0.00 38.97 1.52
4481 8129 6.006449 AGAGTGTTTGATGCTACAGGAAAAT 58.994 36.000 0.00 0.00 0.00 1.82
4486 8134 8.296713 GTGTTTGATGCTACAGGAAAATAAAGA 58.703 33.333 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.045634 TCACTCATGCTGGCAGGC 60.046 61.111 17.64 9.25 0.00 4.85
37 38 1.000396 GCAAGAGGCATCCCAACCT 60.000 57.895 0.00 0.00 43.97 3.50
66 67 3.290710 CAGGGGGAATTGATCGAACAAT 58.709 45.455 14.50 14.50 41.43 2.71
67 68 2.722094 CAGGGGGAATTGATCGAACAA 58.278 47.619 10.73 10.73 0.00 2.83
68 69 1.681780 GCAGGGGGAATTGATCGAACA 60.682 52.381 0.00 0.00 0.00 3.18
69 70 1.025041 GCAGGGGGAATTGATCGAAC 58.975 55.000 0.00 0.00 0.00 3.95
70 71 0.463654 CGCAGGGGGAATTGATCGAA 60.464 55.000 0.00 0.00 0.00 3.71
71 72 1.146041 CGCAGGGGGAATTGATCGA 59.854 57.895 0.00 0.00 0.00 3.59
72 73 0.748005 AACGCAGGGGGAATTGATCG 60.748 55.000 0.00 0.00 0.00 3.69
73 74 0.740737 CAACGCAGGGGGAATTGATC 59.259 55.000 0.00 0.00 0.00 2.92
74 75 0.684153 CCAACGCAGGGGGAATTGAT 60.684 55.000 0.00 0.00 0.00 2.57
85 86 0.958091 TGAATTGTTCCCCAACGCAG 59.042 50.000 0.00 0.00 35.44 5.18
99 100 2.357154 CCCTTCCCAGACCGAATGAATT 60.357 50.000 0.00 0.00 0.00 2.17
101 102 0.618458 CCCTTCCCAGACCGAATGAA 59.382 55.000 0.00 0.00 0.00 2.57
103 104 1.452108 GCCCTTCCCAGACCGAATG 60.452 63.158 0.00 0.00 0.00 2.67
104 105 1.616628 AGCCCTTCCCAGACCGAAT 60.617 57.895 0.00 0.00 0.00 3.34
153 155 0.665835 TTGTCGTTCGCATTTGGCTT 59.334 45.000 0.00 0.00 41.67 4.35
162 164 2.158143 CGTGATTTGATTGTCGTTCGC 58.842 47.619 0.00 0.00 0.00 4.70
326 328 1.085091 GCACACCTCTCAAGCATCTG 58.915 55.000 0.00 0.00 0.00 2.90
342 344 2.287644 GCCTTGGAAATTTGTTGTGCAC 59.712 45.455 10.75 10.75 0.00 4.57
414 416 9.974980 GTCAAATCAAGTTATGTTTCCCTAAAA 57.025 29.630 0.00 0.00 0.00 1.52
455 458 6.145338 TCTGTTCTTCAACTACTCGTTCTT 57.855 37.500 0.00 0.00 32.27 2.52
457 460 5.978322 AGTTCTGTTCTTCAACTACTCGTTC 59.022 40.000 0.00 0.00 32.27 3.95
489 492 8.047310 CCATGGGTTTATCTTGTAGAGTTAACT 58.953 37.037 8.13 8.13 0.00 2.24
490 493 7.201705 GCCATGGGTTTATCTTGTAGAGTTAAC 60.202 40.741 15.13 0.00 0.00 2.01
632 3643 4.013050 GGAAGAAGATGAGTGGGAAAAGG 58.987 47.826 0.00 0.00 0.00 3.11
698 3713 2.315925 AGTGATTGGTAGCGACATGG 57.684 50.000 0.00 0.00 0.00 3.66
823 3838 2.048127 AAGAAGAGGCGCCGTGTC 60.048 61.111 23.20 18.82 0.00 3.67
847 3862 1.813178 CCGAGAAAAGAAAAGGGAGGC 59.187 52.381 0.00 0.00 0.00 4.70
918 3935 2.202676 CTCGCCAAGACTCTCCGC 60.203 66.667 0.00 0.00 0.00 5.54
1241 4259 0.893727 ACCACCAGATTTTCCGGCAC 60.894 55.000 0.00 0.00 0.00 5.01
1282 4300 0.466189 ATAGCGGGGCCACAATCAAG 60.466 55.000 5.46 0.00 0.00 3.02
1297 4315 5.414360 TCTTGTGATTGACAGAGACATAGC 58.586 41.667 0.00 0.00 35.44 2.97
1305 4323 6.547141 AGGAACAAAATCTTGTGATTGACAGA 59.453 34.615 0.00 0.00 45.25 3.41
1330 4348 7.818997 TCGCTTCTCTATCTCTACCAAAATA 57.181 36.000 0.00 0.00 0.00 1.40
1415 4433 7.148306 ACGGCAAAAGGACTTAGTAACATAATG 60.148 37.037 0.00 0.00 0.00 1.90
1437 4460 2.223971 ACATACAGCTACATGGTACGGC 60.224 50.000 10.54 0.00 0.00 5.68
1451 4474 8.494347 GCAAGCAATAGAAGATTAGACATACAG 58.506 37.037 0.00 0.00 0.00 2.74
1475 4498 1.021202 GTAGCGCACCCAATTATGCA 58.979 50.000 11.47 0.00 42.17 3.96
1476 4499 1.264288 GAGTAGCGCACCCAATTATGC 59.736 52.381 11.47 0.00 38.52 3.14
1549 4572 5.365133 CGCGCATTTTAAAATCATAATGCC 58.635 37.500 10.53 5.69 46.18 4.40
1672 4696 0.819582 AATGAGCAAAAGGCCATCGG 59.180 50.000 5.01 0.00 46.50 4.18
1675 4699 3.325716 ACTTCAAATGAGCAAAAGGCCAT 59.674 39.130 5.01 0.00 46.50 4.40
1722 4746 0.036164 ACAGACCAATAAGCGTGCCA 59.964 50.000 0.00 0.00 0.00 4.92
1758 4782 6.543465 ACAAATTTGACAAGAGATGACTCACA 59.457 34.615 24.64 0.00 44.79 3.58
1762 4786 5.334414 GCGACAAATTTGACAAGAGATGACT 60.334 40.000 24.64 0.00 0.00 3.41
1800 4828 6.875195 TCGTCGTTAACAAGGATCCTAATTTT 59.125 34.615 16.55 8.37 0.00 1.82
1904 4932 9.777297 AAGTCCTGCAAACAAACATAATTTAAT 57.223 25.926 2.10 0.00 0.00 1.40
2052 5080 2.887152 AGCCTTCTGTTTAACCAGCAAG 59.113 45.455 0.00 1.19 32.32 4.01
2097 5125 2.368875 CCACCCTACAGAAGACAAGTGT 59.631 50.000 0.00 0.00 0.00 3.55
2268 5296 7.549839 TCCCTTCATTCAGCATTCAATTAAAG 58.450 34.615 0.00 0.00 0.00 1.85
2270 5298 7.664552 ATCCCTTCATTCAGCATTCAATTAA 57.335 32.000 0.00 0.00 0.00 1.40
2353 5381 6.291955 GCATACATGACAGCATTTACATTTGC 60.292 38.462 0.00 0.00 39.17 3.68
2373 5401 2.736670 AGACTCAAATGGGGGCATAC 57.263 50.000 0.00 0.00 0.00 2.39
2577 5636 6.073222 AGCACTAGAAACAAAATAAGTCGTGG 60.073 38.462 0.00 0.00 0.00 4.94
2615 5674 9.708222 CAACAATTATCTATACAGCACAAGAAC 57.292 33.333 0.00 0.00 0.00 3.01
2674 5733 2.103094 CTCTGAAACCGGATGGATAGCA 59.897 50.000 9.46 0.00 39.21 3.49
2876 5937 2.547218 GCAAACACGGTCCTGAGAGTTA 60.547 50.000 0.00 0.00 0.00 2.24
2906 5968 6.375455 GGTGTCTTATGAACACTTTGATCCAT 59.625 38.462 6.38 0.00 35.00 3.41
2928 5990 3.809279 GGCAAAGAACAATCAAAAGGGTG 59.191 43.478 0.00 0.00 0.00 4.61
2929 5991 3.454082 TGGCAAAGAACAATCAAAAGGGT 59.546 39.130 0.00 0.00 0.00 4.34
2932 5994 9.044150 TCTATTTTGGCAAAGAACAATCAAAAG 57.956 29.630 13.04 0.00 37.46 2.27
2934 5996 7.984050 TGTCTATTTTGGCAAAGAACAATCAAA 59.016 29.630 13.04 0.00 0.00 2.69
2939 6001 8.177119 AGTATGTCTATTTTGGCAAAGAACAA 57.823 30.769 13.04 0.00 0.00 2.83
2982 6044 1.732259 GGACACTCCTGCAACATAACG 59.268 52.381 0.00 0.00 32.53 3.18
2986 6048 0.108585 AACGGACACTCCTGCAACAT 59.891 50.000 0.00 0.00 33.30 2.71
3010 6072 4.038763 TGTGTTTCACGAACTGTAGGAGAT 59.961 41.667 0.00 0.00 39.08 2.75
3016 6078 4.384547 CGATGATGTGTTTCACGAACTGTA 59.615 41.667 0.00 0.00 39.08 2.74
3017 6079 3.184379 CGATGATGTGTTTCACGAACTGT 59.816 43.478 0.00 0.00 39.08 3.55
3055 6117 1.655885 TCGTGCTTTTCGAGACGGA 59.344 52.632 0.00 0.00 33.02 4.69
3128 6190 6.878923 TGACCGTTCAAATGTAAGATCAGAAT 59.121 34.615 0.00 0.00 0.00 2.40
3130 6192 5.789521 TGACCGTTCAAATGTAAGATCAGA 58.210 37.500 0.00 0.00 0.00 3.27
3131 6193 6.480524 TTGACCGTTCAAATGTAAGATCAG 57.519 37.500 0.00 0.00 38.87 2.90
3132 6194 5.106712 GCTTGACCGTTCAAATGTAAGATCA 60.107 40.000 0.00 0.00 41.34 2.92
3133 6195 5.324697 GCTTGACCGTTCAAATGTAAGATC 58.675 41.667 0.00 0.00 41.34 2.75
3134 6196 4.142902 CGCTTGACCGTTCAAATGTAAGAT 60.143 41.667 0.00 0.00 41.34 2.40
3135 6197 3.185594 CGCTTGACCGTTCAAATGTAAGA 59.814 43.478 0.00 0.00 41.34 2.10
3136 6198 3.479006 CGCTTGACCGTTCAAATGTAAG 58.521 45.455 0.00 0.00 41.34 2.34
3137 6199 2.350007 GCGCTTGACCGTTCAAATGTAA 60.350 45.455 0.00 0.00 41.34 2.41
3138 6200 1.195900 GCGCTTGACCGTTCAAATGTA 59.804 47.619 0.00 0.00 41.34 2.29
3156 6218 1.717645 GCACATTCAAAGAAAGCAGCG 59.282 47.619 0.00 0.00 0.00 5.18
3174 6236 3.494924 TAAGTTCTCTTCAGCAAGCTGCA 60.495 43.478 16.89 5.68 43.31 4.41
3198 6262 3.234386 GTTTCTGTAAAGCAATGTCCGC 58.766 45.455 0.00 0.00 0.00 5.54
3211 6275 3.390135 CGAACCTGCTCTTGTTTCTGTA 58.610 45.455 0.00 0.00 0.00 2.74
3244 6308 4.883354 GCCAGGGGATTGGGAGCG 62.883 72.222 0.00 0.00 38.72 5.03
3245 6309 4.883354 CGCCAGGGGATTGGGAGC 62.883 72.222 0.00 0.00 38.72 4.70
3385 6449 6.352737 GGGGGTTATCACATCAGAAACTAGAA 60.353 42.308 0.00 0.00 0.00 2.10
3407 6473 0.111253 AGGTTTGTCTCTGCAAGGGG 59.889 55.000 0.00 0.00 32.73 4.79
3506 6572 3.114616 CGGCGTCTTGTGAGCAGG 61.115 66.667 0.00 0.00 0.00 4.85
3536 6602 4.461431 TCCAAGTAATTGTAGAGCGACTCA 59.539 41.667 1.80 0.00 32.06 3.41
3625 6693 7.811653 TGAGATCTCGAACATCATATGTACTC 58.188 38.462 17.76 0.00 44.07 2.59
3626 6694 7.663493 TCTGAGATCTCGAACATCATATGTACT 59.337 37.037 17.76 0.00 44.07 2.73
3627 6695 7.748683 GTCTGAGATCTCGAACATCATATGTAC 59.251 40.741 17.76 0.00 44.07 2.90
3628 6696 7.094592 GGTCTGAGATCTCGAACATCATATGTA 60.095 40.741 21.91 0.88 44.07 2.29
3630 6698 6.092092 GGTCTGAGATCTCGAACATCATATG 58.908 44.000 21.91 0.00 0.00 1.78
3660 6728 7.173907 ACACAAGCTATATGTATGAAGGAATGC 59.826 37.037 0.00 0.00 0.00 3.56
3693 6761 5.221283 TGCATTGCATCTATAAACACATGGG 60.221 40.000 7.38 0.00 31.71 4.00
3710 6778 1.337703 TGGTGTTTCTGTCTGCATTGC 59.662 47.619 0.46 0.46 0.00 3.56
3774 6842 5.316167 TCATCTGAGCACTGTATTTGGTTT 58.684 37.500 0.00 0.00 0.00 3.27
3811 6879 5.011329 GGAAATGGATGTATGTGATGGCATT 59.989 40.000 0.00 0.00 0.00 3.56
3843 6911 8.375506 TGTATTTGGTATTAAGATCTAGGCCAG 58.624 37.037 5.01 0.00 0.00 4.85
3882 6950 4.277476 ACAAACAGAGGAAAATGACACCA 58.723 39.130 0.00 0.00 0.00 4.17
3883 6951 4.918810 ACAAACAGAGGAAAATGACACC 57.081 40.909 0.00 0.00 0.00 4.16
3904 6972 1.990799 CGACAAGATCGCCAACAGTA 58.009 50.000 0.00 0.00 45.52 2.74
3955 7023 2.093288 CCACTGATGCTACCACTGACAT 60.093 50.000 0.00 0.00 0.00 3.06
4081 7404 0.900647 AGCGACCTAGCAAGTGTCCT 60.901 55.000 0.00 0.00 40.15 3.85
4103 7426 2.685017 ACTGGGATGCGCAGAGGA 60.685 61.111 18.32 0.00 45.41 3.71
4104 7427 2.513204 CACTGGGATGCGCAGAGG 60.513 66.667 18.32 6.66 45.41 3.69
4105 7428 1.812922 GTCACTGGGATGCGCAGAG 60.813 63.158 18.32 11.44 45.41 3.35
4106 7429 2.265739 GTCACTGGGATGCGCAGA 59.734 61.111 18.32 2.04 45.41 4.26
4108 7431 4.408821 GGGTCACTGGGATGCGCA 62.409 66.667 14.96 14.96 0.00 6.09
4182 7508 3.218453 TGCACGGAAGGAAATGAAGAAA 58.782 40.909 0.00 0.00 0.00 2.52
4189 7515 3.091545 ACATGATTGCACGGAAGGAAAT 58.908 40.909 0.00 0.00 0.00 2.17
4192 7518 1.003003 TGACATGATTGCACGGAAGGA 59.997 47.619 0.00 0.00 0.00 3.36
4203 7529 5.069119 TCGTGTAGAGCCTAATGACATGATT 59.931 40.000 0.00 0.00 32.52 2.57
4209 7535 6.255596 TCATATCGTGTAGAGCCTAATGAC 57.744 41.667 0.00 0.00 0.00 3.06
4218 7544 7.993821 AAACAAGACATCATATCGTGTAGAG 57.006 36.000 0.00 0.00 37.74 2.43
4221 7547 7.709182 CCCTAAAACAAGACATCATATCGTGTA 59.291 37.037 0.00 0.00 37.74 2.90
4229 7555 5.640147 TGGTTCCCTAAAACAAGACATCAT 58.360 37.500 0.00 0.00 29.42 2.45
4230 7556 5.055265 TGGTTCCCTAAAACAAGACATCA 57.945 39.130 0.00 0.00 29.42 3.07
4288 7614 3.272766 GCAAAGGTTGGCTGAACAC 57.727 52.632 2.29 0.00 36.12 3.32
4307 7910 1.812571 CGAAAGGAGAACCCACAATGG 59.187 52.381 0.00 0.00 37.41 3.16
4315 7918 0.253327 ATGCCCTCGAAAGGAGAACC 59.747 55.000 5.34 0.00 46.67 3.62
4343 7946 4.022416 TGAAAATGGAAGGTGAAATGGACG 60.022 41.667 0.00 0.00 0.00 4.79
4379 7982 5.563592 TGAGAATCCTGCAAATCAAAGAGA 58.436 37.500 0.00 0.00 0.00 3.10
4429 8034 2.289072 CCTATAGGATTCGTGTGGGCAG 60.289 54.545 14.11 0.00 37.39 4.85
4437 8053 7.125356 ACACTCTTAAAACCCTATAGGATTCGT 59.875 37.037 21.07 6.47 39.89 3.85
4438 8054 7.498443 ACACTCTTAAAACCCTATAGGATTCG 58.502 38.462 21.07 5.78 39.89 3.34
4451 8067 7.041372 TCCTGTAGCATCAAACACTCTTAAAAC 60.041 37.037 0.00 0.00 0.00 2.43
4455 8071 5.738619 TCCTGTAGCATCAAACACTCTTA 57.261 39.130 0.00 0.00 0.00 2.10
4456 8072 4.623932 TCCTGTAGCATCAAACACTCTT 57.376 40.909 0.00 0.00 0.00 2.85
4505 8153 6.763355 TCATAGGAAATCTAGCATCAACTCC 58.237 40.000 0.00 0.00 0.00 3.85


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.